Installation of Collector version 1.5.0
July 2017
Before you start
----------------
You need to have installed in your system
- Java Development Kit 8 (Oracle JDK7)
If you don't have this software installed you can download the latest version from here:
http://www.oracle.com/technetwork/java/javase/downloads/index.html
The easiest way to install is to download the tgz file and extract it to a suitable place (for example /opt).
Alternatively, you can download a version of Collector with a bundled 64bit JDK distribution
- PostgreSQL 8.4 or higher
If you don't have this version installed you can download it from here:
http://www.enterprisedb.com/products-services-training/pgdownload
The easiest way is to use the graphical installer. It installs postgresql, configures it to start with the system and creates a postgres user.
We will assume that you have PostgresSQL installed at "/opt/PostgreSQL/9.2", and a user "postgres" with a password "postgres". If you have changed any of these settings please introduce the correct settings in the step 2 below.
Installation procedure
----------------------
1. Extract the contents of collector_bin.tgz to a suitable place. For example /opt/collector
2. Define the correct settings in the file environment. In particular:
COLLECTOR_HOME=/opt/collector # the location of collector
JAVA_HOME=$COLLECTOR_HOME/jdk # the location of JDK. We assume we will use the bundled JDK. If not modify accordingly.
JDK_KEYSTORE_PWD=changeit # JDK default keystore value
PGPASSWORD=postgres # the password of the user postgresexport
PG_HOME=/opt/PostgreSQL/9.2 # Location of Postgres installation
4. Execute the install script
./install
That's all!
If the installation completed successfully you can test it executing directly collector
./collector
You must see the following text appear in the screen:
Collector v1.4.6
Usage: collector [newjobuniprotid|executejob|listfilters|listprotocols|listjobs|listjobexecutions|export|deletejob|deletejobexecution|deletejobexecutionsforjobid] [options]
Command: newjobuniprotid [options]
newjobuniprotid is a command.
--protocolid
protocolid is Int property.
--uniprotid
uniprotid is string property.
--jobdescription
jobdescription is String property.
Command: executejob [options]
executejob is a command.
--jobdescription
jobdescription is a string property.
Command: listfilters
listfilters is a command.
Command: listprotocols
listprotocols is a command.
Command: listjobs
listjobs is a command.
Command: listjobexecutions [options]
listjobexecutions is a command.
--jobid
jobid is a integer property
Command: export [options]
export data to file
--raw
raw is a flag
--jobexecutionid
jobexecutionid is a integer property
--datatoexport
datatoexport must be "activities" or "compounds"
--exportformat
exportformat must be "sdf" or "csv"
--filename
filename is a string
Command: deletejob [options]
deletejob is a command.
--jobid
jobid is a integer property.
Command: deletejobexecution [options]
deletejobexecution is a command.
--jobexecutionid
jobexecutionid is a integer property.
Command: deletejobexecutionsforjobid [options]
deletejobexecutionsforjobid is a command.
--jobid
jobid is a integer property.
If you have any problem with the installation, contact us at the following e-mail addresses:
Manuel Pastor manuel.pastor@upf.edu
Oriol L. Masasaguer oriol.lopez@upf.edu